Koon and her Master, Saldith, met with the Council, and Koon informed the Masters of the Council that her uncle wanted to speak with them. Saldith reassured the Council that Koon's mind was calm and told the Jedi Council member Mace Windu that he had felt it best to approach the Council on this matter, since Saldith knew that the Kel Dor species communicated with their minds. The Councilors joined their minds with Koon's, contacting Plo Koon and the Jedi on Troiken. After speaking with Plo Koon, the Council sent a Jedi strike force to assist his team, which ultimately helped to bring a resolution to the Stark Hyperspace War.[2]

When Koon's forces arrived on Bal'demnic, they found the planet in chaos, with the native Kon'mespeciesrebelling against the Confederacy. After the clonetroopers landed, the Kon'me became furious and attacked all of the off-worlders. Although Koon and her forces were forced to retreat from Bal'demnic, the Confederacy also halted its mining operation on the planet. After the battle, the Republic assigned a fleet to protect Bal'demnic from further Separatist operations.[5] Later that year, Koon and Baylis Archan were sent with a command of clones to the planet Giju. A battle ensued with the Separatists, and both Koon's forces and her Padawan were killed. After the battle and Archan's demise, Koon returned to Coruscant to recover from her wounds, particularly one to her right eye, and to meditate on her actions. She refused to return to the war.[1]

Koon awoke to find members of the Grand Army of the Republic's 501st Legionattacking the Jedi Temple. The clones she ran into attacked her, and Koon deflected their blaster bolts with her lightsaber. While fleeing the soldiers, Koon witnessed Jedi Knight Anakin Skywalker—who had recently been christened as the Sith Lord Darth Vader—kill Jocasta Nu. Koon felt Skywalker's emotions and immediately realized that he had fallen to the dark side and joined the Sith. Koon then fled from Vader and his legion by way of the secret passageways under the Jedi Temple that she had learned from Padawan Jin-Lo Rayce.[1]

"Im…pressive. But…to kill me…you must now…face me.""Gladly. Killer of younglings. Betrayer of friends. Destroyer of the Jedi to whom you claimed allegiance. Animal. I have longed for this day.""As have I. With your death…my mission is complete. You…are the last…"

As time passed by in the Coruscant Underworld, Koon befriended a group of zombie-like creatures called Cthons. She plotted to cripple the newly crownedEmperor Palpatine, the instigator of the Great Jedi Purge, by defeating his Sith apprentice, Darth Vader. Koon eventually contacted Palpatine over his secure holographic channel and lied to the Emperor, expressing her desire to become his Sith apprentice by offering to eliminate Vader. Although Palpatine was not deceived by Koon, he sent Vader to the Jedi Temple underlevels to confront her.[1]

Sha Koon is killed by Darth Vader.

After Vader—who was forced to wear a suit of life-preserving armor due to previous injuries dealt to him by Jedi Master Obi-Wan Kenobi[6]—arrived in the underlevels, Koon was surprised to find that the person under Vader's mask was Anakin Skywalker. Vader recognized Koon's emotions and commented that he would have killed Koon if she had chosen not to flee during his raid on the Jedi Temple. Vader also stated that Palpatine saw through Koon's lies, claiming that Koon had only spoke via holocomm to hide her true intent of killing Palpatine. Koon revealed to Vader that her fallback plan was to cripple Palpatine by killing his Sith apprentice instead. With that, Koon unleashed the Cthons on Vader.[1]

As the creatures attacked the Dark Lord of the Sith, Koon explained that they were easily controlled by the Force. The Cthons then threw an electroshock net on Vader, which damaged the life support systems on his armor. Vader broke free of the net and killed the Cthons, remarking that while the attempt was impressive, Koon had to face Vader then and there. The two combatants ignited their lightsabers, and Koon stated that she had been waiting to face him. Vader asserted that with her death, his mission to eliminate all the Jedi would be complete and added that she was the last Jedi alive to oppose the Sith.[1]

As Koon and Darth Vader began a lightsaber duel, Koon contemplated the Sith Lord's claim that she was the last surviving Jedi. She became all the more determined to kill Vader, feeling that no one else would be able to do so if she failed. Koon was able to injure the Dark Lord by slashing him across his chest. Vader eventually gained the upper hand by gripping her throat with the Force. Vader then impaled Koon through the chest. Before she died, Koon experienced a vision through the Force of a rebellion against the Galactic Empire, Vader redeeming himself by killing Emperor Palpatine, and the rebirth of the Jedi Order through Vader's children, Luke Skywalker and Leia Organa. Realizing that the future did not depend on her, Koon died at peace.[1]

"Your emotions reveal you, Sha Koon. Yes, I remember you from that day in the Archives. I would have killed you then, but you chose to flee. My Master bid me come here. You want to kill me and take my place. Or so you said. Your lie amused Lord Sidious. You spoke via holocomm to hide your true intent—to kill him. Your plan is as pathetically simple as it is doomed.""I have a fallback plan. Cripple him by killing you."

To the Kel Dor female Sha Koon, a telepath's images were more than words—they were bits of melody or explosions of feeling. She viewed her uncle's mind as rich and textured, yet full of contradictions. Yet, she knew that Plo Koon understood himself and what it meant to be a Jedi. After she rose to the rank of Jedi Knight, Koon was given a Padawan named Baylis Archan. Training Archan seemed natural to Koon, since Archan also possessed telepathic gifts. Koon viewed Archan's mind as playful, similar to a fast-moving river, and felt that Archan's thoughts were like fish in that river, darting and sparkling.[1]

Before her death at Darth Vader's hands, Sha Koon experienced a vision of Luke Skywalker's New Jedi Order.

Koon believed that the Clone Wars were a violent and needless war. After her Padawan died in battle with the Separatists on Giju, she refused to return to combat against the Confederacy. When Darth Vader attacked the Jedi Temple, Koon chose to flee her attackers and was determined not to be killed like a mindless beast. Before Koon dueled Vader underneath the Jedi Temple, she told the Sith that she believed him to be a murderer of children, a traitor to his friends, and a destroyer of the Jedi to whom he was once allied. She expressed her desire to face Vader, and the Sith replied that Koon was the last Jedi and that his mission to eliminate every Jedi would be complete with her death.[1]

After hearing this, Koon felt that her success in killing Vader was of the utmost importance—as she believed that if she was unable to defeat Vader, no one else would be able to and the Sith would rule the galaxy. Before Koon died from the fatal injury dealt to her by Vader, she initially saw her death as the mark of her mission's failure. After she experienced a vision depicting the Emperor's death, Vader's redemption, and the Jedi Order's rebirth through Vader's children, she realized that the future of the galaxy did not depend on her and died at peace with herself.[1]

Sha Koon possessed telepathic abilities and had a strong telepathic bond with her uncle, Plo Koon. When her uncle came to Dorin for her, she knew without a word being said that he had come to take her to Coruscant's Jedi Temple so that she could begin her training.[1] Near the end of the Stark Hyperspace War, Koon was able to receive a telepathic contact from her uncle all the way from the planet Troiken while she herself was on Coruscant.[2] When Order 66 was initiated, Koon sensed her uncle's death and temporarily slipped into unconsciousness. During the assault on the Jedi Temple led by Anakin Skywalker—who had taken up the mantle of Darth Vader—Koon was able to read Skywalker's thoughts and determine that he had joined the Sith. Before they dueled in the underlevels of the Jedi Temple, Koon used her telepathic abilities to confirm that Vader was Anakin Skywalker.[1]

Koon was able to utilize the ability to telekinetically push her enemies away with the Force and was capable of using the Force to control the Cthons, who were easily dominated with the Force. She was also skilled in the use of a lightsaber and wounded Darth Vader before he gained the upper hand in their duel. Before she died, Koon had a vision through the Force that depicted future events.[1]